Contacts of the strand formed by residues 125 - 133 (chain A) in PDB entry 1GNG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.7 33.8 - - + +
89A GLN 3.3 12.6 - - - +
90A ASP* 4.6 5.8 - - + -
91A LYS* 4.0 6.4 + - - +
120A GLY* 3.0 24.3 + - - -
121A GLU 5.4 0.2 + - - -
122A LYS* 2.7 59.3 + - + +
123A LYS* 3.3 3.1 + - - +
124A ASP* 1.3 86.5 - - - +
126A VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.5 4.5 - - - +
89A GLN* 2.6 53.8 + - + +
91A LYS* 3.5 43.3 - - + +
117A TYR* 4.2 29.2 - - + -
118A SER 3.8 13.9 - - - +
119A SER* 5.6 0.7 - - - -
120A GLY* 4.2 2.9 - - - +
125A GLU* 1.3 73.0 - - - +
127A TYR* 1.3 60.5 + - - +
128A LEU 4.0 0.2 - - - -
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Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS* 3.6 38.6 - - + -
87A VAL 3.0 18.6 - - - +
88A LEU* 3.4 38.4 - - + +
117A TYR* 3.4 5.0 - - - -
118A SER* 2.9 35.7 + - - -
119A SER 3.5 25.6 - - - -
120A GLY* 3.9 12.6 - - - -
121A GLU* 4.5 10.3 + - + +
126A VAL* 1.3 73.4 - - - +
128A LEU* 1.3 60.2 + - - +
129A ASN* 3.2 6.4 + - - -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS 3.2 4.5 - - - +
86A LYS* 3.3 2.8 - - - -
87A VAL* 2.9 33.7 + - + +
89A GLN* 4.9 7.3 - - + +
95A ASN* 3.6 28.7 - - + +
98A LEU* 3.4 37.0 - - + -
115A PHE* 3.8 22.9 - - + -
116A PHE 3.7 6.7 - - - +
117A TYR* 3.7 32.9 - - + +
126A VAL 4.0 2.0 + - - -
127A TYR* 1.3 73.6 - - - +
129A ASN* 1.3 68.1 + - - +
130A LEU* 3.8 16.6 - - + +
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 5.8 0.2 - - - -
84A ILE* 4.1 9.8 - - + +
85A LYS 3.4 3.4 - - - -
86A LYS* 3.3 29.6 - - - +
115A PHE* 3.2 23.8 - - - -
116A PHE* 2.7 52.3 + - + +
118A SER* 3.0 27.1 + - - -
127A TYR 3.2 20.8 + - - -
128A LEU* 1.3 73.9 - - - +
130A LEU* 1.3 64.2 + - - +
131A VAL* 3.3 5.7 + - - +
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 3.2 3.1 - - - -
85A LYS* 2.9 55.7 + - + +
87A VAL* 4.6 9.2 - - + -
95A ASN* 5.6 0.9 - - - +
97A GLU* 3.8 37.2 - - + +
98A LEU* 4.4 19.5 - - + +
101A MET* 4.7 9.6 - - + -
112A LEU* 3.8 17.7 - - + -
114A TYR 4.0 0.4 - - - -
115A PHE* 4.4 1.8 - - - -
128A LEU* 3.8 28.9 - - + +
129A ASN* 1.3 70.9 - - - +
131A VAL* 1.3 61.9 + - - +
132A LEU* 3.4 16.2 + - + +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 5.9 4.0 - - + -
56A TYR* 6.4 0.4 - - + -
75A LEU* 5.1 6.1 - - + -
82A VAL* 3.7 30.5 - - + -
83A ALA 3.4 3.1 - - - +
84A ILE* 4.0 14.4 - - + +
112A LEU* 3.7 1.3 - - - +
113A ARG* 2.9 36.4 + - + +
114A TYR* 2.9 33.5 + - + +
116A PHE* 3.6 34.3 - - + -
129A ASN 3.6 4.3 - - - +
130A LEU* 1.3 69.0 - - - +
132A LEU* 1.3 58.1 + - - +
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 2.9 28.1 - - - +
83A ALA* 2.7 23.0 + - + +
85A LYS* 4.7 21.3 - - + -
97A GLU* 5.5 4.9 - - - +
101A MET* 4.2 23.1 - - + -
110A VAL* 4.3 14.1 - - + -
111A ARG 3.7 8.5 - - - +
112A LEU* 3.8 22.9 - - + -
113A ARG* 4.4 0.7 - - - -
130A LEU* 4.0 19.1 - - + +
131A VAL* 1.3 73.6 - - - +
133A ASP* 1.3 68.0 + - - +
199A CYS* 6.2 0.9 - - + -
200A ASP* 5.7 7.4 - - - +
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLU* 4.3 2.4 - - - +
81A LEU 4.6 1.7 - - - +
82A VAL* 4.3 4.8 - - - +
83A ALA* 4.2 5.3 - - - +
110A VAL* 3.5 24.6 - - + +
111A ARG* 2.8 55.0 + - - +
113A ARG* 3.4 28.6 + - - +
132A LEU* 1.3 79.0 - - - +
134A TYR* 1.3 62.6 + - - +
135A VAL* 4.0 7.0 + - + -
188A LEU* 4.5 5.4 - - - +
197A LYS* 5.7 8.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il